Suzuki-Miyaura cross-coupling is a well-known method for making biaryls. With bifunctional monomers, Suzuki polycondensation (SPC) can be used to make polyaryls. Given the complexity of the reacting solution, studying the mechanism of SPC is extremely tough. To solve this problem, we used tandem mass spectrometric (MS/MS) methods to observe the dynamic behaviour of catalytically relevant species in real time. Catalysis involves a complex soup of reactants, intermediates and products. We used an ESI-MS with a triple quadrupole mass analyzer to monitor the SPC in positive ion mode using pressurized sample infusion (PSI) in real time. Full scan, selected ion recording (SIR), product ion scan, neutral loss scan (NLS) and multiple reaction monitoring (MRM) MS/MS methods were applied. Tetrakistriphenylphosphine palladium(0) was the catalyst of this reaction and a positively charged phosphonium aryl iodide tag (m/z 478) was implemented into the first catalytic cycle, enabling us to track all the intermediate oligomers up to the 4th addition. Product ion scan revealed all the intermediate oligomers lose a triphenylphosphine fragment (m/z 262) which would either come from the complex or the charged tag. Three significant intermediate types were observed in each stage of the catalysis, oxidative addition, transmetallation and reductive elimination and their behavior was studied in a chronogram, normalized to the total ion current. As expected, the use of selected ion recording, and neutral loss scan dramatically improved the signal-to-noise ratio. Ultimately, multiple reaction monitoring showed the best chronogram data due to the fact that this scan acts as a “double filter” in a soup of reactive species and contaminants. Real time reaction monitoring has proven to provide detailed insights regarding a reaction. MS/MS methods are promising for improving data quality, selectivity and sensitivity in reaction monitoring. The principle is broadly applicable to other systems, from an intricate catalytic reaction with short-lived ionic intermediates to a reaction with only a single product generated. Reaction dynamics for an exceptionally complex reaction can be made simple and easy by utilizing tandem mass spectrometry methods in time resolved reaction monitoring. / Graduate

Glyco-oxidation is linked to the pathophysiology of diabetes and diabetic complications. The process of glyco-oxidation generates reactive dicarbonyls, which form adducts on arginine residues in distributions throughout the proteome that are site-specific depending on the protein microenvironment. Dicarbonyl adducts are thus markers for glyco-oxidative stress. Various approaches using mass spectrometry permits the identification, localization, and quantification of these dicarbonyl adducts. Using MG as a model dicarbonyl, a shotgun proteomics approach identified the sites for modification of major plasma proteins. Thirty five sites on seven abundant plasma proteins were found, and investigation into the microenvironment surrounding the target arginine sites revealed a neighboring charged residue motif where adjacent residues were either negatively or positively charged. One of the sites identified was R257 in HSA, which is located in the important drug binding site I. We validated drug site I as a target for MG modification by the adaptation of two assays to monitor the effect of MG modification. MG significantly decreases the rate of hydrolysis of PGE2 in drug site I, and induces the displacement of prodan from drug site I. Molecular modeling of warfarin docking at drug site I with the MG-modified R257 resulted in significantly decreased binding and change in binding orientation. The oxidation products of susceptible residues methionine, tryptophan, and cysteine were evaluated using MRM of oxidized HSA peptides. Oxidation of methionine gave the M+16 single oxidized product, and M329 in HSA was the most responsive site. Oxidation of the sole W214 tryptophan produced the W+32 double oxidation product, and oxidation of C34 produced the C+48 triple oxidation product. MG, 3DG, and glucosone were evaluated for propensity to modify 12 HSA sites based on MRM of dicarbonyl modified HSA. Dicarbonyl modification was independent of arginine solvent accessibility. In a clinical study using nephropathy as an endpoint, sites of oxidation and modification of HSA by MG, 3DG, and glucosone were quantified by MRM. The most important variable among diabetic subjects was metformin use, and subjects taking metformin had significantly reduced markers for glyco-oxidation. These findings may be useful in the development of new diabetes therapies that aim to ameliorate glyco-oxidative stress.

Electrospray ionization (ESI) facilitates the transfer of ions in solution into the gas-phase for analysis by mass spectrometry. The ionization process is intricate and required further investigation, especially because of the lack of in-depth literature on the subject. Furthermore, investigations into the ESI process will serve to assist development of real-time reaction monitoring. To do this, a cationic ionic liquid, butyl methylimidazolium, [BMIM]+, was paired with several counterions and mixed in various solvents. This was analyzed by ESI mass spectrometry to determine the relative response ratio between two observable aggregates. The findings assisted in the elucidation of differential surface activity of chemically distinct ions in ESI, with respect to changes in solvent. Furthermore, the results obtained suggested acetonitrile is an optimal solvent for the analysis of ions of this type due to a reduction in differential effects, whereas other common ESI solvents prove to enhance the surface activity of specific aggregate ions. Further investigations into ESI-MS involved effects of spray head geometry relative to the inlet to the mass spectrometer. The position of the spray-head, the solvent, and additional instrumental parameters were independently adjusted during the analysis of an equimolar mixture of two different ions. It was found that these parameters have dramatic effects on the distribution of signal intensity from one ion to another, and therefore the resulting usefulness of acquired spectra. The sharp contrast in ion intensity, and even differential ion activity, with relatively minor instrument changes (such as temperature programming, gas flow rates and solvent choice) demonstrated the importance of finding the optimal spot for the ESI spray head, especially when signal intensity and a quality analysis is key. Additional ESI-MS work involved working with an industry partner to develop selective charge-tagging reagents for the characterization of petroleum fractions by ESI-MS. A simple chemical derivatization technique was developed in which thiols and disulfides may be selectively analyzed in a complex matrix and easily characterized. These reagents enhanced detection of thiols and disulfides solely due to the nature of the charged tag derivatization agent. The charged disulfides readily and exclusively react with thiols in a complex matrix in a short amount of time. The synthesis of these reagents was simple and resulted in a pure and stable reagent. The efficacy of the reaction was demonstrated using on-line monitoring, while the scope and usefulness of the reaction was demonstrated in petroleum fractions. A combination of UV-Vis spectroscopy and electrospray ionization mass spectrometry was used for real-time monitoring of Pd2(dba)3 activation with sulfonated versions of PPh3 and a Buchwald-type ligand. This provides insight into the effect of ligand and preparation conditions on activation and allows for establishment of rational activation protocols. It is expected that this reaction monitoring technique will be enhanced through the use of tandem mass spectrometry. Finally, an experimental method of visualizing atomic orbitals was developed as a demonstration intended for first year chemistry students. This demonstration involved the examination of nodal and anti-nodal regions of Chladni figures which students could then connect to the concept of quantum mechanical parameters and their relationship to atomic orbital shape. / Graduate

Le nombre croissant de médicaments protéiques utilisés en thérapeutique a créé des besoins dans le domaine de leur quantification, principalement dans le plasma, un milieu de composition protéique complexe. Le dosage, essentiel aux études pharmacocinétique/pharmacodynamique, ainsi qu’à l’optimisation de ces traitements, est compliqué par la nature protéique de ces médicaments et par les faibles concentrations auxquelles ils sont attendus dans ces milieux complexes. La méthodologie proposée se démarque des méthodes de dosage usuelles par son caractère universel. Elle fait appel à la spectrométrie de masse adaptée à la quantification des protéines grâce à l’utilisation d’un marquage isotopique différentiel des peptides : après enrichissement et protéolyse, l’échantillon à doser est marqué sur les lysines par la version légère d’un réactif de dérivation. En parallèle, les peptides de la protéine médicament pure marqués par la version lourde du réactif, servent d’étalon interne. La possibilité de quantifier la protéine à partir de plusieurs de ses peptides améliore la fiabilité du dosage. Appliquée à l’epoetin beta aux concentrations attendues en thérapeutique (autour de 0,5 femtomole/µL de plasma), la stratégie proposée permet de situer la limite de quantification à environ 50 attomoles d’epoetin beta/µL de plasma avec une méthodologie de spectrométrie de masse nano-LC-ESI-Q-TRAP fonctionnant en mode MRM. Pour étendre l’universalité de cette approche au champ des protéines médicaments pégylées, une seconde molécule a été étudiée. Il s’agit de l’interféron alfa-2b pégylé qui a permis de mettre en place une stratégie d’extraction spécifique du médicament utilisant sa pégylation. / The growing number of therapeutic proteins has created needs in the field of their quantification, mainly in plasma, which is a complex protein environment. Quantitative analysis of these proteins is essential for pharmacokinetics/pharmacodynamics studies, and for the optimization of treatments. However, the nature itself of the analyte and the low concentrations that are expected in plasma complicate the quantitative analysis. The proposed methodology differs from usual methods on its universal applicability. It relies on mass spectrometry adapted to the quantification of proteins by using peptides differential isotope labelling : after enrichment and proteolysis, the therapeutic protein and the plasmatic proteins are labelled on lysine residues by the light reagent. In parallel, peptides of the pure therapeutic protein, labelled by heavy version of reagent, are used as internal standard. The ability to quantify the protein with several of its peptides improves the reliability of the analysis. When applied to epoetin beta at expected therapeutic concentrations (about 0.5 femtomole/µL of plasma), the proposed strategy leads to a quantification limit close to 50 attomoles of epoetin beta/µL plasma, with a nano-LC-ESI-Q-TRAP mass spectrometry methodology operating in MRM. To extend the universal character of this approach to the field of pegylated protein drugs, a second therapeutic protein model has been studied. This model is a pegylated interferon alfa-2b which allowed developing a strategy for specific extraction of the drug relying on its pegylation.

Les cytochromes P450 (CYPs) jouent un rôle essentiel dans le métabolisme oxydatif de nombreux composés endogènes et exogènes. L’expression de CYPs est extrêmement variable en fonction de facteurs physiopathologiques, génétiques et environnementaux. Le métabolisme des xénobiotiques par les CYPs dépend en partie de la nature, de la quantité et de l’activité d’isoformes des CYPs impliqués. L'analyse quantitative de l'expression de CYP dans les organes du métabolisme, tels que le foie, sont d'une importance particulière étant donné que la biotransformation réalisée par les CYPs est souvent un facteur critique qui affecte l'efficacité, la disponibilité et la toxicité des médicaments chez l'homme. La technique actuelle de dosage la plus courante est l’immunoquantification par Western Blot. Cette technique est limitée par la disponibilité et la spécificité de l'anticorps. Les techniques de protéomique par spectrométrie de masse, permettant d’analyser de très faibles quantités de protéines en mélange, sont les méthodes de choix pour l’identification et la quantification des CYPs dans différents organes. Nous avons développé et validé une méthode pour doser 6 CYPs (1A2, 2C9, 2D6, 2J2, 3A4 et 3A5) par spectrométrie de masse en couplage chromatographique. Cette méthode, simple, rapide de sensibilité satisfaisante et peu coûteuse, a été validée dans différents types de matrices biologiques (lignées cellulaires hépatiques et neuronales, baculosomes). Ensuite, elle a été appliquée à grande échelle pour l’analyse de 50 foies humains (microsomes et mitochondries) afin d’étudier la relation phénotype/génotype pour les CYPs. Cette méthode pourra être appliquée à d’autres CYPS, est un outil utile qui permettra d’améliorer la compréhension et la prédiction pharmacocinétique et toxique de médicaments et d’autres produits chimiques. / Cytochromes P450 (CYPs) play a key role in the oxidative metabolism of many endogenous and exogenous compounds. The expression of CYPs is extremely variable depending on patho-physiological, genetic and environmental factors. The metabolism of xenobiotics by CYPs depends on the nature the quantity and the activity of CYP isoforms involved. Quantitative analysis of CYP expression in organs such as liver, are of particular importance since the biotransformation performed by CYPs is often a critical factor that affects the efficiency, availability and drug toxicity in humans. The most common technique is the immune-quantitation (Western Blot). This technique is limited by the availability and specificity of the antibody. Mass spectrometry-based proteomics, able to analyze very small amounts of protein in a mixture, are the methods of choice for identification and quantification of CYPs in different organs. We developed and validated a method for dosing 6 CYPs (1A2, 2C9, 2D6, 2J2, 3A4 and 3A5) by liquid chromatography coupled with mass spectrometry. This simple, rapid, low-cost method has an adequate sensitivity, and has been validated in different types of biological matrices (liver and neuronal cell lines, baculosomes). It has been applied at large-scale to analyze these 6 CYPs in 50 human livers samples (microsomes and mitochondria) to study the phenotype/genotype relationship. This method, which could easily be applied to other CYPs, provides an important tool to improve the understanding and prediction of pharmacokinetics and toxicity profile of drugs and other chemicals.

Ion mobility (IM) spectrometry is a gas-phase electrophoretic technique in which ions are separated on the basis of their relative mobility in the presence of a weak electric field gradient and a buffer gas. Ion mobility-mass spectrometry (IM-MS) has the capability of separating ions based on m/z, size and shape, providing additional structural information compared to using mass spectrometry on its own. In this thesis, IM-MS has been used to investigate organic and organometallic complexes and identify reactants, intermediates and products in reaction mixtures. Collision cross sections (CCS) have been measured for three salen ligands, and their complexes with copper and zinc using travelling-wave ion mobility-mass spectrometry (TWIMS) and drift tube ion mobility-mass spectrometry (DTIMS), allowing a comparative size evaluation of the ligands and complexes. CCS measurements using TWIMS were determined using peptide and TAAH calibration standards with good intra-day and inter-day reproducibility. TWIMS measurements gave significantly larger CCS than DTIMS derived data in helium, indicating that the choice of calibration standards is important in ensuring the accuracy of TWIMS derived CCS measurements. The CCS data obtained from IM-MS measurements have been compared to CCS values obtained from X-ray coordinates and modelled structures. The analysis of small organic and organometallic molecules has been extended to investigations of the potential of IM-MS for reaction monitoring and structural studies of the components of catalytic cycles. Reaction mixtures of an organocatalysed Diels-Alder cycloaddition reaction have been monitored using IM-MS and high-field asymmetric waveform ion mobility-mass spectrometry (FAIMS-MS). Reactant, product, catalyst and reaction intermediates, including an intermediate not previously detected, were identified and the catalyst and intermediates monitored over time. An organometallic catalytic cycle using a palladium catalyst has been analysed using IM-MS and the CCS of reactants, intermediates and products have been measured and compared to theoretical CCS calculations. Good agreement was observed between measured and calculated data. Species not amenable to electrospray ionisation were covalently bound to an ionisable tag containing a quaternary ammonium ion allowing the tagged molecules to be detected by IM-MS.

The World Health Organization has called stress-related illness “the health epidemic of the 21st century.” While the biochemical pathways associated with the acute stress response are well-characterized, many of the pathways behave differently under conditions of chronic stress. The purpose of this project is to apply high-sensitivity mass spectrometry (MS)-based targeted and untargeted metabolomics approaches to generate new insights into the biochemical processes and pathways associated with the chronic stress response, and potential mechanisms by which chronic stress produces adverse health effects. Chapter 1 describes the application of sets of targeted and untargeted metabolomics approaches to analyze serum samples from a human epigenetic model of chronic stress in order to identify potential targets for further analysis. To test the resulting hypothesis that oxidative stress is a key feature of chronic stress, a new targeted multiple reaction monitoring (MRM)-MS assay was developed for the accurate quantitation of aldehyde products of lipid peroxidation, as described in Chapter 2. In Chapter 3, the validated method for quantitation of malondialdehyde (MDA) was t applied to mouse plasma samples from a model of chronic social defeat stress to determine whether animals exposed to psychosocial stress show increases in oxidative stress. Mouse plasma samples from this model were also analyzed by untargeted metabolomics using Fourier-transform (FT)-MS to identify other important metabolite features, particularly those that overlap with metabolites identified in the human epigenetic model. Analysis of metabolomic data from two very different models of chronic stress supports the consistent detection of a metabolomic phenotype for chronic stress that is characterized by the dysregulation of energy metabolism associated with decreased concentrations of diacyl-phospholipids in blood. Increased blood concentrations of fatty acids, carnitines, acylcarnitines, and ether phospholipids were also observed. In addition to metabolites associated with energy metabolism, chronic stress also significantly influenced metabolites associated with amino acid metabolism and cell death. This characteristic pattern of differences in metabolite concentrations was observed in the plasma of mice exposed to chronic social defeat stress, irrespective of whether or not they displayed outward signs of a chronic stress response; In fact, mice that were “resilient” to the behavioural effects of chronic social defeat stress displayed an exaggerated phenotype over mice that showed depressive-like symptoms following chronic stress exposure. This may suggest that the observed changes in fatty acid composition are protective against stress. However, changes in fatty acid composition are also known to be associated with a wide variety of pathologies including heart disease, neurodegenerative diseases, and mood disorders, so the lipidomic changes associated with chronic stress may also contribute to its health impact. Overall, the results provide further evidence that changes in energy metabolism are a central part of allostatic adaptation to chronic stress. / Graduate / 0487 / csobsey@gmail.com

Protein engineering strategies, such as directed evolution, generate large libraries of enzyme variants, typically in the range of 106-108 variants. However, the availability of rapid, robust high-throughput screening methods has often limited the impact of directed evolution in discovering enzymes with enhanced catalyst performance. Raman spectroscopy is an established analytical technique, providing molecular specific information, permitting analysis in aqueous solutions and as such is an attractive, alternative screening method for biological systems. Although an inherently weak physical phenomenon, enhanced Raman scattering techniques, such as surface enhanced Raman scattering (SERS) and ultraviolet resonance Raman (UVRR) spectroscopy, can be used to overcome the associated sensitivity issues. Herein, we successfully monitored xanthine oxidase (XO) catalysed conversions of xanthine to uric acid, before extending to hypoxanthine, using two contrasting Raman scattering enhanced approaches. Firstly, a SERS-based assay was developed utilising silver nanoparticles to measure analytes directly and quantitatively on micromolar scale, in the absence of chromogenic substrates or lengthy chromatography. Secondly, a UVRR approach was developed enabling monitoring of the XO-mediated reaction in real-time and without the need to quench the system. Significantly, both methods demonstrated over &gt;30 fold reduction in acquisition times (when compared to conventional HPLC analysis), and offered excellent medium-term reproducibility and accuracy of results over significant time periods. Furthermore, investigations were made into developing this SERS-based assay into an enantiomeric screen using another vibrational spectroscopy approach, Raman optical activity (ROA), along with circular dichroism (CD). Successful chiral reduced nanoparticles were synthesised, with multiple characterisation techniques employed, affording enantiopure Au-cysteine and Ag-tyrosine colloids. However, it was not possible to generate consistent and reproducible SEROA responses, with these techniques ultimately being unsuccessful in analysing these chiral sensitive nanoprobes, and thus differentiating between the D- and L- forms. Finally, a novel SERS-based approach, in combination with the standard addition method (SAM), was developed for the routine analysis of uric acid (end product in XO catalysed reaction(s) and biomarker for various diseases), at clinically relevant levels in urine samples from patients. Results were highly comparable and in very good agreement with HPLC analyses, with an average < 9% difference in predictions between the two analytical approaches across all samples analysed, and a 60-fold reduction in acquisition time (when compared with HPLC). Together, the research presented in this thesis demonstrates the suitability of Raman enhanced techniques for quantitative analysis, measuring the analytes directly using a portable Raman instrument and, most importantly, offering significant reductions in acquisition times when compared to established analytical techniques.

Protein tyrosine nitration (PTN) is a posttranslational modification resulting from oxidative/nitrosative stress that has been implicated in a wide variety of disease states. Characterization of PTN is challenging due to several factors including its low abundance in a given proteome, preferential site modification, multiple target site proximity within unique peptide sequences, and analytical method and instrument limitations. Current analytical techniques are insufficiently sensitive to identify endogenous nitration sites without incorporation of either nitrotyrosine or target protein enrichment. However, enrichment proficiency can also be inadequate. Chemical derivatization of the nitro- moiety can be incomplete or result in undesirable byproduct formation, while immunoaffinity proficiency is contingent upon antibody specificity. To overcome analytical method and enrichment deficiencies, we aimed to develop a comprehensive nitroproteome-specific workflow using molecular methods combined with mass spectrometry. Our approach was to systematically address all relevant factors contributing to PTN such as primary sequence, protein conformation, solvent accessibility, and nitrating agent concentration. Our ultimate goal was to increase mass spectrometric sensitivity for PTN identification. All putative nitroprotein/nitropeptide identifications were then subjected to rigorous validation by either manual spectrum analyses or peptide synthesis. We further developed MS methods for quantitation of nitropeptides from complex mixtures with minimal sample processing. Successful application of our nitroproteome-specific mass spectrometric workflow is expected to provide powerful tools for comprehensive PTN investigation that will elucidate its role in the onset and progression of a variety of disease states as well as facilitate discovery of therapeutic targets.

Bis(dimethylamino)-2-(4-methoxyphenyl)naphthalene (3) and 1,8-bis(dimethylamino)-4-diphenylphosphonaphthalene (5b) were synthesized as ESI-active analogues of the common organometallic ligands η6-anisole and triphenylphosphine. The water-soluble phosphine, sodium triphenylphosphine monosulfonate, was re-purposed as an ESI-active ligand. Its solubility in organic solvents and amenability to electrospray ionization was improved by replacing Na+ with the non-coordinating bis(triphenylphosphine)iminium cation. A new sample introduction method named PSI (pressurized sample infusion) was developed for the continuous infusion of air/moisture-sensitive samples into the mass spectrometer. The flow rate can be determined using a modified version of the Hagen-Poiseuille equation, and the ability of PSI (coupled with an ESI tag) to give quantitative kinetic data is demonstrated. A method for maintaining a dry, air-free ESI source is described for the analysis of highly reactive samples. The above developments were applied to the study of the copper-free Sonogashira (Heck alkynylation) reaction. The proposed active catalyst (Pd(0)L2, where L = PPh3 or 7) was observed, and its reactivity with iodomethane in the gas phase was determined to be less than that of Pd(0)L. Nevertheless, Pd(0)L2 is extremely reactive and even oxidatively adds dichloromethane (t1/2 = 10.7 min at 40 °C). Under standard reaction conditions intermediates corresponding to oxidative addition and transmetallation were detected, and coordination of base to palladium was observed for secondary amines but not triethylamine. Reductive elimination was achieved in the gas phase for a series of para-substituted aryl iodides with phenylacetylene, and the slope of the resulting Hammett plot (ρ) was -0.5. No evidence for the previously hypothesized anionic mechanism was observed. Simultaneous kinetic analysis of charged substrate, products and intermediates in the copper-free Sonogashira reaction was conducted using PSI-ESI-MS and high quality, information rich data for each species over time was obtained. In the absence of protons, reductive elimination is rate-limiting and the rate of reaction is relatively high. In the presence of protons (a byproduct of the reaction), transmetallation is rate-limiting and the rate of reaction is much slower. The use of a strong base was shown to improve the efficiency of the reaction, and an experimentally-derived catalytic cycle for the copper-free Sonogashira reaction is proposed. / Graduate